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- PDB-1zlm: Crystal structure of the SH3 domain of human osteoclast stimulati... -

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Basic information

Entry
Database: PDB / ID: 1zlm
TitleCrystal structure of the SH3 domain of human osteoclast stimulating factor
ComponentsOsteoclast stimulating factor 1
KeywordsSIGNALING PROTEIN / Beta barrel
Function / homology
Function and homology information


ossification / SH3 domain binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / signal transduction / extracellular region
Similarity search - Function
SH3 Domains / SH3 domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Src homology 3 domains ...SH3 Domains / SH3 domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Osteoclast-stimulating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsChen, L. / Wang, Y. / Wells, D. / Toh, D. / Harold, H. / Zhou, J. / DiGiammarino, E. / Meehan, E.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution.
Authors: Chen, L. / Wang, Y. / Wells, D. / Toh, D. / Harold, H. / Zhou, J. / DiGiammarino, E. / Meehan, E.J.
History
DepositionMay 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Osteoclast stimulating factor 1


Theoretical massNumber of molelcules
Total (without water)6,7411
Polymers6,7411
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.810, 80.480, 49.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-198-

HOH

21A-201-

HOH

DetailsThe asymmetric unit contains one monomer which is the biological unit.

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Components

#1: Protein Osteoclast stimulating factor 1


Mass: 6741.462 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSTF1 / Plasmid: pET28-OSF-SH3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92882
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium Hepes, PEG400, ammonium sulfate, pH 7.5, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 16, 2004
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.07→31.1 Å / Num. all: 28252 / Num. obs: 27403 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 17.4
Reflection shellResolution: 1.07→1.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1612 / Rsym value: 0.241 / % possible all: 49.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GRI

1gri


Resolution: 1.07→10 Å / Num. parameters: 5467 / Num. restraintsaints: 6382 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5%
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 1333 0 %RANDOM
Rwork0.1582 ---
all0.1599 27365 --
obs0.158 27365 82.7 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 607
Refinement stepCycle: LAST / Resolution: 1.07→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms477 0 0 130 607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0274
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.045
X-RAY DIFFRACTIONs_approx_iso_adps0.082

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